Kuzu migration notes (#1149)

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## Description
<!-- Provide a clear description of the changes in this PR -->

## DCO Affirmation
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the terms of the Topoteretes Developer Certificate of Origin.

alembic/versions/b9274c27a25a_kuzu_11_migration.py

@@ -9,6 +9,12 @@ Create Date: 2025-07-24 17:11:52.174737
 import os
 from typing import Sequence, Union
 
+from cognee.infrastructure.databases.graph.kuzu.kuzu_migrate import (
+    kuzu_migration,
+    read_kuzu_storage_version,
+)
+import kuzu
+
 # revision identifiers, used by Alembic.
 revision: str = "b9274c27a25a"
 down_revision: Union[str, None] = "e4ebee1091e7"
@@ -18,34 +24,43 @@ depends_on: Union[str, Sequence[str], None] = None
 
 def upgrade() -> None:
     # This migration is only for multi-user Cognee mode
-    if not os.getenv("ENABLE_BACKEND_ACCESS_CONTROL", "false").lower() == "true":
-        return
+    if os.getenv("ENABLE_BACKEND_ACCESS_CONTROL", "false").lower() == "true":
+        from cognee.base_config import get_base_config
 
-    from cognee.base_config import get_base_config
+        base_config = get_base_config()
 
-    base_config = get_base_config()
+        databases_root = os.path.join(base_config.system_root_directory, "databases")
+        if not os.path.isdir(databases_root):
+            raise FileNotFoundError(f"Directory not found: {databases_root}")
 
-    databases_root = os.path.join(base_config.system_root_directory, "databases")
-    if not os.path.isdir(databases_root):
-        raise FileNotFoundError(f"Directory not found: {databases_root}")
+        for current_path, dirnames, _ in os.walk(databases_root):
+            # If file is kuzu graph database
+            if ".pkl" in current_path[-4:]:
+                kuzu_db_version = read_kuzu_storage_version(current_path)
+                if (
+                    kuzu_db_version == "0.9.0" or kuzu_db_version == "0.8.2"
+                ) and kuzu_db_version != kuzu.__version__:
+                    # Try to migrate kuzu database to latest version
+                    kuzu_migration(
+                        new_db=current_path + "_new",
+                        old_db=current_path,
+                        new_version=kuzu.__version__,
+                        old_version=kuzu_db_version,
+                        overwrite=True,
+                    )
+    else:
+        from cognee.infrastructure.databases.graph import get_graph_config
 
-    for current_path, dirnames, _ in os.walk(databases_root):
-        # If file is kuzu graph database
-        if ".pkl" in current_path[-4:]:
-            from cognee.infrastructure.databases.graph.kuzu.kuzu_migrate import (
-                kuzu_migration,
-                read_kuzu_storage_version,
-            )
-            import kuzu
-
-            kuzu_db_version = read_kuzu_storage_version(current_path)
+        graph_config = get_graph_config()
+        if graph_config.graph_database_provider.lower() == "kuzu":
+            kuzu_db_version = read_kuzu_storage_version(graph_config.graph_file_path)
             if (
                 kuzu_db_version == "0.9.0" or kuzu_db_version == "0.8.2"
             ) and kuzu_db_version != kuzu.__version__:
                 # Try to migrate kuzu database to latest version
                 kuzu_migration(
-                    new_db=current_path + "new",
-                    old_db=current_path,
+                    new_db=graph_config.graph_file_path + "_new",
+                    old_db=graph_config.graph_file_path,
                     new_version=kuzu.__version__,
                     old_version=kuzu_db_version,
                     overwrite=True,

cognee/infrastructure/databases/graph/kuzu/adapter.py

@@ -86,12 +86,11 @@ class KuzuAdapter(GraphDBInterface):
                     if (
                         kuzu_db_version == "0.9.0" or kuzu_db_version == "0.8.2"
                     ) and kuzu_db_version != kuzu.__version__:
-                        # TODO: Write migration script that will handle all user graph databases in multi-user mode
                         # Try to migrate kuzu database to latest version
                         from .kuzu_migrate import kuzu_migration
 
                         kuzu_migration(
-                            new_db=self.db_path + "new",
+                            new_db=self.db_path + "_new",
                             old_db=self.db_path,
                             new_version=kuzu.__version__,
                             old_version=kuzu_db_version,
@@ -1464,11 +1463,8 @@ class KuzuAdapter(GraphDBInterface):
         It raises exceptions for failures occurring during deletion processes.
         """
         try:
-            # Use DETACH DELETE to remove both nodes and their relationships in one operation
-            await self.query("MATCH (n:Node) DETACH DELETE n")
-            logger.info("Cleared all data from graph while preserving structure")
-
             if self.connection:
+                self.connection.close()
                 self.connection = None
             if self.db:
                 self.db.close()

cognee/infrastructure/databases/graph/kuzu/kuzu_migrate.py

@@ -94,6 +94,7 @@ def ensure_env(version: str, export_dir) -> str:
 
     print(f"→ Setting up venv for Kùzu {version}...", file=sys.stderr)
     # Create venv
+    # NOTE: Running python in debug mode can cause issues with creating a virtual environment from that python instance
     subprocess.run([sys.executable, "-m", "venv", base], check=True)
     # Install the specific Kùzu version
     subprocess.run([py_bin, "-m", "pip", "install", "--upgrade", "pip"], check=True)